bioconductor.org "GenomeAnnotation" keyword
View the packages on the bioconductor.org package registry that are tagged with the "GenomeAnnotation" keyword.
Top 0.5% on bioconductor.org
9 versions - Latest release: 3 months ago - 183 dependent packages - 4.27 million downloads total - 1 maintainer
GenomicFeatures 1.62.0
Query the gene models of a given organism/assembly9 versions - Latest release: 3 months ago - 183 dependent packages - 4.27 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
8 versions - Latest release: 3 months ago - 54 dependent packages - 1.71 million downloads total - 1 maintainer
HDF5Array 1.38.0
HDF5 datasets as array-like objects in R8 versions - Latest release: 3 months ago - 54 dependent packages - 1.71 million downloads total - 1 maintainer
Top 1.8% on bioconductor.org
8 versions - Latest release: 3 months ago - 14 dependent packages - 415 thousand downloads total - 2 maintainers
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data8 versions - Latest release: 3 months ago - 14 dependent packages - 415 thousand downloads total - 2 maintainers
Top 0.2% on bioconductor.org
21 versions - Latest release: 2 months ago - 342 dependent packages - 10.6 million downloads total - 1 maintainer
GenomeInfoDb 1.46.2
Utilities for manipulating chromosome names, including modifying them to follow a particular nami...21 versions - Latest release: 2 months ago - 342 dependent packages - 10.6 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
10 versions - Latest release: 2 months ago - 604 dependent packages - 9.23 million downloads total - 1 maintainer
GenomicRanges 1.62.1
Representation and manipulation of genomic intervals10 versions - Latest release: 2 months ago - 604 dependent packages - 9.23 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
8 versions - Latest release: 3 months ago - 111 dependent packages - 7.73 million downloads total - 1 maintainer
DelayedArray 0.36.0
A unified framework for working transparently with on-disk and in-memory array-like datasets8 versions - Latest release: 3 months ago - 111 dependent packages - 7.73 million downloads total - 1 maintainer
Top 5.0% on bioconductor.org
6 versions - Latest release: 2 months ago - 1 dependent package - 103 thousand downloads total - 1 maintainer
microRNA 1.68.0
Data and functions for dealing with microRNAs6 versions - Latest release: 2 months ago - 1 dependent package - 103 thousand downloads total - 1 maintainer
VariantExperiment 1.24.0
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend7 versions - Latest release: 3 months ago - 9.75 thousand downloads total - 1 stars on GitHub - 1 maintainer
GenomicDistributions 1.18.0
GenomicDistributions: fast analysis of genomic intervals with Bioconductor6 versions - Latest release: 3 months ago - 11.9 thousand downloads total - 1 maintainer
UCSC.utils 1.6.1
Low-level utilities to retrieve data from the UCSC Genome Browser5 versions - Latest release: about 1 month ago - 2 dependent packages - 1.39 million downloads total - 1 maintainer
Top 5.4% on bioconductor.org
6 versions - Latest release: 3 months ago - 4 dependent packages - 77.4 thousand downloads total - 52 stars on GitHub - 1 maintainer
QDNAseq 1.46.0
Quantitative DNA Sequencing for Chromosomal Aberrations6 versions - Latest release: 3 months ago - 4 dependent packages - 77.4 thousand downloads total - 52 stars on GitHub - 1 maintainer
scPipe 2.10.0
Pipeline for single cell multi-omic data pre-processing6 versions - Latest release: 3 months ago - 24.9 thousand downloads total - 69 stars on GitHub - 1 maintainer
nullranges 1.16.3
Generation of null ranges via bootstrapping or covariate matching7 versions - Latest release: about 1 month ago - 1 dependent package - 15.4 thousand downloads total - 22 stars on GitHub - 1 maintainer
compEpiTools 1.44.0
Tools for computational epigenomics6 versions - Latest release: 2 months ago - 24.9 thousand downloads total - 1 maintainer
COCOA 2.24.0
Coordinate Covariation Analysis6 versions - Latest release: 2 months ago - 14.7 thousand downloads total - 1 maintainer
HelloRanges 1.36.0
Introduce *Ranges to bedtools users6 versions - Latest release: 2 months ago - 2 dependent packages - 31.4 thousand downloads total - 1 maintainer
mCSEA 1.30.1
Methylated CpGs Set Enrichment Analysis8 versions - Latest release: about 1 month ago - 1 dependent package - 17 thousand downloads total - 1 maintainer
ASpli 2.20.0
Analysis of Alternative Splicing Using RNA-Seq6 versions - Latest release: 2 months ago - 1 dependent package - 28.8 thousand downloads total - 1 maintainer
branchpointer 1.35.1
Prediction of intronic splicing branchpoints6 versions - Latest release: 2 months ago - 17.2 thousand downloads total - 1 maintainer
SMITE 1.38.0
Significance-based Modules Integrating the Transcriptome and Epigenome6 versions - Latest release: 3 months ago - 18.5 thousand downloads total - 1 stars on GitHub - 2 maintainers
fcScan 1.24.0
fcScan for detecting clusters of coordinates with user defined options6 versions - Latest release: 2 months ago - 13.8 thousand downloads total - 1 maintainer
Top 8.3% on bioconductor.org
6 versions - Latest release: 3 months ago - 5 dependent packages - 105 thousand downloads total - 194 stars on GitHub - 1 maintainer
EnrichedHeatmap 1.40.0
Making Enriched Heatmaps6 versions - Latest release: 3 months ago - 5 dependent packages - 105 thousand downloads total - 194 stars on GitHub - 1 maintainer
IWTomics 1.34.1
Interval-Wise Testing for Omics Data7 versions - Latest release: 7 days ago - 17.4 thousand downloads total - 1 maintainer
MIRA 1.32.0
Methylation-Based Inference of Regulatory Activity6 versions - Latest release: 2 months ago - 1 dependent package - 17.7 thousand downloads total - 1 maintainer
LOLA 1.40.1
Locus overlap analysis for enrichment of genomic ranges7 versions - Latest release: 7 days ago - 5 dependent packages - 41.4 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
6 versions - Latest release: 2 months ago - 2 dependent packages - 127 thousand downloads total - 1 maintainer
GreyListChIP 1.42.0
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs6 versions - Latest release: 2 months ago - 2 dependent packages - 127 thousand downloads total - 1 maintainer
plotgardener 1.16.0
Coordinate-Based Genomic Visualization Package for R11 versions - Latest release: 3 months ago - 4 dependent packages - 21.8 thousand downloads total - 335 stars on GitHub - 2 maintainers
txdbmaker 1.6.2
Tools for making TxDb objects from genomic annotations9 versions - Latest release: about 1 month ago - 8 dependent packages - 167 thousand downloads total - 1 maintainer
Top 5.5% on bioconductor.org
6 versions - Latest release: 2 months ago - 62.4 thousand downloads total - 1 maintainer
MEDIPS 1.62.0
DNA IP-seq data analysis6 versions - Latest release: 2 months ago - 62.4 thousand downloads total - 1 maintainer
AssessORF 1.28.0
Assess Gene Predictions Using Proteomics and Evolutionary Conservation6 versions - Latest release: 2 months ago - 15.8 thousand downloads total - 1 maintainer
Top 6.0% on bioconductor.org
14 versions - Latest release: 7 days ago - 3 dependent packages - 183 thousand downloads total - 67 stars on GitHub - 1 maintainer
tximeta 1.28.2
Transcript Quantification Import with Automatic Metadata14 versions - Latest release: 7 days ago - 3 dependent packages - 183 thousand downloads total - 67 stars on GitHub - 1 maintainer
NoRCE 1.22.0
NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment6 versions - Latest release: 2 months ago - 10.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.6% on bioconductor.org
6 versions - Latest release: 3 months ago - 1 dependent package - 56.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
Organism.dplyr 1.37.1
dplyr-based Access to Bioconductor Annotation Resources6 versions - Latest release: 3 months ago - 1 dependent package - 56.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 0.2% on bioconductor.org
7 versions - Latest release: 3 months ago - 632 dependent packages - 7.61 million downloads total - 1 maintainer
SummarizedExperiment 1.40.0
A container (S4 class) for matrix-like assays7 versions - Latest release: 3 months ago - 632 dependent packages - 7.61 million downloads total - 1 maintainer
plyxp 1.4.3
Data masks for SummarizedExperiment enabling dplyr-like manipulation6 versions - Latest release: 2 months ago - 4.05 thousand downloads total - 4 stars on GitHub - 1 maintainer
HilbertCurve 2.4.1
Making 2D Hilbert Curve7 versions - Latest release: about 2 months ago - 1 dependent package - 24.4 thousand downloads total - 42 stars on GitHub - 1 maintainer
atSNP 1.26.0
Affinity test for identifying regulatory SNPs6 versions - Latest release: 3 months ago - 15.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
BREW3R.r 1.6.0
R package associated to BREW3R5 versions - Latest release: 3 months ago - 4.89 thousand downloads total - 0 stars on GitHub - 1 maintainer
bambu 3.12.1
Context-Aware Transcript Quantification from Long Read RNA-Seq data11 versions - Latest release: 22 days ago - 1 dependent package - 31.9 thousand downloads total - 217 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
6 versions - Latest release: 3 months ago - 3 dependent packages - 79.4 thousand downloads total - 90 stars on GitHub - 1 maintainer
rGREAT 2.12.1
GREAT Analysis - Functional Enrichment on Genomic Regions6 versions - Latest release: 3 months ago - 3 dependent packages - 79.4 thousand downloads total - 90 stars on GitHub - 1 maintainer
GrafGen 1.6.0
Classification of Helicobacter Pylori Genomes4 versions - Latest release: 2 months ago - 4.64 thousand downloads total - 1 maintainer
Seqinfo 1.0.0
A simple S4 class for storing basic information about a collection of genomic sequences1 version - Latest release: 3 months ago - 361 thousand downloads total - 1 maintainer
stPipe 1.0.1
Upstream pre-processing for Sequencing-Based Spatial Transcriptomics2 versions - Latest release: 2 months ago - 887 downloads total - 4 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
14 versions - Latest release: 2 months ago - 2 dependent packages - 195 thousand downloads total - 1 maintainer
DMRcate 3.6.0
Methylation array and sequencing spatial analysis methods14 versions - Latest release: 2 months ago - 2 dependent packages - 195 thousand downloads total - 1 maintainer
pram 1.26.0
Pooling RNA-seq datasets for assembling transcript models6 versions - Latest release: 3 months ago - 10.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
geneXtendeR 1.36.0
Optimized Functional Annotation Of ChIP-seq Data6 versions - Latest release: 2 months ago - 20.1 thousand downloads total - 9 stars on GitHub - 1 maintainer
HiCPotts 1.0.0
HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C1 version - Latest release: 3 months ago - 799 downloads total - 0 stars on GitHub - 1 maintainer
garfield 1.38.0
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction6 versions - Latest release: 2 months ago - 15.7 thousand downloads total - 1 maintainer
BSgenomeForge 1.10.2
Forge your own BSgenome data package11 versions - Latest release: about 1 month ago - 1 dependent package - 16.4 thousand downloads total - 1 maintainer
Top 6.8% on bioconductor.org
6 versions - Latest release: 2 months ago - 6 dependent packages - 88.7 thousand downloads total - 25 stars on GitHub - 1 maintainer
annotatr 1.36.0
Annotation of Genomic Regions to Genomic Annotations6 versions - Latest release: 2 months ago - 6 dependent packages - 88.7 thousand downloads total - 25 stars on GitHub - 1 maintainer
RCAS 1.36.0
RNA Centric Annotation System7 versions - Latest release: 3 months ago - 1 dependent package - 23 thousand downloads total - 1 maintainer
planttfhunter 1.10.0
Identification and classification of plant transcription factors6 versions - Latest release: 3 months ago - 5.94 thousand downloads total - 1 stars on GitHub - 1 maintainer
PICB 1.2.0
piRNA Cluster Builder2 versions - Latest release: 3 months ago - 2.39 thousand downloads total - 5 stars on GitHub - 1 maintainer
ODER 1.6.0 removed
Optimising the Definition of Expressed Regions1 version - Latest release: over 2 years ago - 1.01 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
4 versions - Latest release: over 1 year ago - 255 dependent packages - 6.49 million downloads total - 1 maintainer
AnnotationDbi 1.68.0
Manipulation of SQLite-based annotations in Bioconductor4 versions - Latest release: over 1 year ago - 255 dependent packages - 6.49 million downloads total - 1 maintainer
InterMineR 1.26.0 removed
R Interface with InterMine-Powered Databases4 versions - Latest release: almost 2 years ago - 12 thousand downloads total - 17 stars on GitHub - 1 maintainer
DeepBlueR 1.27.0 removed
DeepBlueR2 versions - Latest release: about 2 years ago - 12.8 thousand downloads total - 3 maintainers
STAN 2.28.0 removed
The Genomic STate ANnotation Package1 version - Latest release: over 2 years ago - 14.8 thousand downloads total - 1 maintainer
Related Keywords
Software
58
Sequencing
33
Annotation
21
Coverage
19
Genetics
14
DataImport
14
Visualization
14
ImmunoOncology
13
RNASeq
12
FunctionalGenomics
11
Infrastructure
11
ChIPSeq
10
GeneExpression
10
DataRepresentation
9
Preprocessing
9
DifferentialExpression
8
GenomeAssembly
8
Transcriptomics
8
GeneRegulation
7
QualityControl
7
SequenceMatching
7
DNAMethylation
6
Microarray
6
GeneSetEnrichment
6
Epigenetics
6
SingleCell
5
GO
5
SystemsBiology
5
Transcription
5
MultipleComparison
5
Alignment
5
HiddenMarkovModel
4
DifferentialMethylation
4
FunctionalPrediction
4
MethylSeq
3
MethylationArray
3
Classification
3
rna-seq
3
MotifAnnotation
3
r
3
StatisticalMethod
3
DifferentialPeakCalling
3
genomics
3
bioconductor
3
GenomeWideAssociation
3
GeneTarget
3
Pathways
2
transcriptomics
2
Clustering
2
ChipOnChip
2
PeakDetection
2
CpGIsland
2
ComparativeGenomics
2
GenePrediction
2
Proteomics
2
annotation
2
VariantAnnotation
2
BiologicalQuestion
2
SNP
2
bioconductor-package
2
CopyNumberVariation
2
WholeGenome
2
TimeCourse
2
ATACSeq
2
AlternativeSplicing
2
TwoChannel
2
DNaseSeq
2
HistoneModification
2
Spatial
2
Regression
2
GenomicVariation
2
genome-annotation
2
epigenetics
1
computational-biology
1
chip-seq
1
ThirdPartyClient
1
c
1
bioinformatics
1
NaturalLanguageProcessing
1
transcript-model
1
r-package
1
matching
1
intermine
1
biology
1
Reactome
1
KEGG
1
transcription-factors
1
rstats
1
protein-domains
1
plants
1
plant-genomics
1
hidden-markov-models
1
gene-families
1
functional-genomics
1
MotifDiscovery
1
GeneFusionDetection
1
Bayesian
1
functional-annotation
1
statistics
1
bootstrap
1